The design of the experiments (table with parameters) can be found here. But here is a brief description.
| PS | N_GENES_INITIAL | BITING_RATE_MEAN | N_LOCI | N_ALLELES_INITIAL |
|---|---|---|---|---|
| 01 | 120 | 0.1 | 2 | 12 |
| 02 | 1200 | 0.2 | 2 | 120 |
| 03 | 12000 | 0.5 | 2 | 1200 |
I kept daily biting rates fixed to 1.
In the complete neutrality, the number of circulating strains seems just too much. This is orders of magnitude more than the selection.
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 9"
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## [1] "PS: 04 | Scenario: S | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 10"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 10"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 10"
The EIR for selection seems too low? For neutrality it is an order of magnitude more.
Notice the order of magnitude difference in the number of repertoires
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
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## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
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## [1] "Scenario: S | exp: 001 | run: 6"
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## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
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## [1] "Scenario: S | exp: 001 | run: 8"
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## [1] "Scenario: S | exp: 001 | run: 9"
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## [1] "Scenario: S | exp: 001 | run: 10"
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## [1] "Scenario: S | exp: 001 | run: 1"
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## [1] "Scenario: S | exp: 001 | run: 3"
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## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
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## [1] "Scenario: S | exp: 001 | run: 8"
## [1] "Scenario: N | exp: 001 | run: 8"
## [1] "Scenario: G | exp: 001 | run: 8"
## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 2"
## [1] "Scenario: N | exp: 001 | run: 2"
## [1] "Scenario: G | exp: 001 | run: 2"
## [1] "Scenario: S | exp: 001 | run: 3"
## [1] "Scenario: N | exp: 001 | run: 3"
## [1] "Scenario: G | exp: 001 | run: 3"
## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
## [1] "Scenario: G | exp: 001 | run: 7"
## [1] "Scenario: S | exp: 001 | run: 8"
## [1] "Scenario: N | exp: 001 | run: 8"
## [1] "Scenario: G | exp: 001 | run: 8"
## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"
Cutoff is based on the selection case, so we will look at it more closely. Then we will compare the behavior of the system across scenarios at different cutoffs.
Persistence (months)
Relative persistence
Persistence (months) Relative persistence
Persistence (months)
Relative persistence
All scenarios:
Compare this to the diversity (wihtout the temporal dimension):